Package fr.ens.biologie.genomique.aozan

Class RunData

  • public class RunData
extends Object
    This class define a RunData object that contains all information generated by collectors.
    Since:
    0.8
    Author:
    Laurent Jourdren

    • Constructor Detail

      • RunData

        public RunData()
        Public constructor.

      • RunData

        public RunData​(RunData data)
        Public constructor.
        Parameters:
        data - Data to add

      • RunData

        public RunData​(File file)
        throws IOException
        Public constructor.
        Parameters:
        file - file to read
        Throws:
        IOException - if an error occurs while reading the data file

    • Method Detail

      • getCollectorNames

        public List<String> getCollectorNames()
        Get the list of collector names.
        Returns:
        a list with the names of the collectors

      • isCollectorEnabled

        public boolean isCollectorEnabled​(String collectorName)
        Test if a collector is enabled.
        Parameters:
        collectorName - name of the collector to test
        Returns:
        true if the collector is enabled

      • getAllSamplesInLane

        public List<Integer> getAllSamplesInLane​(int lane)
        Get all samples names related to the lane as a list.
        Parameters:
        lane - the lane number
        Returns:
        all samples related to the lane

      • getSamplesInLane

        public List<Integer> getSamplesInLane​(int lane)
        Get all samples identifiers (without undetermined samples) related to the lane as a list.
        Parameters:
        lane - the lane number
        Returns:
        all samples related to the lane

      • getAllSamples

        public List<Integer> getAllSamples()
        Get all samples identifiers (with undetermined samples) of the run.
        Returns:
        all samples related to the lane

      • getSamples

        public List<Integer> getSamples()
        Get all samples identifiers (without undetermined samples) of the run.
        Returns:
        all samples related to the lane

      • getSampleCount

        public int getSampleCount()
        Get the sample count.
        Returns:
        the sample count

      • isUndeterminedInLane

        public boolean isUndeterminedInLane​(int lane)
        Check if undetermined FASTQ file exist for a lane.
        Parameters:
        lane - the lane
        Returns:
        true if if undetermined FASTQ file exist for a lane

      • getIndexSample

        public String getIndexSample​(int sampleId)
        Get the sequence index related to a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to sample

      • getSampleIdentifier

        public String getSampleIdentifier​(int sampleId)
        Get the sample identifier string.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • getSampleName

        public String getSampleName​(int sampleId)
        Get the name of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • getSampleDemuxName

        public String getSampleDemuxName​(int sampleId)
        Get the demultiplexing name of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • getSampleLane

        public int getSampleLane​(int sampleId)
        Get the lane of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • isUndeterminedSample

        public boolean isUndeterminedSample​(int sampleId)
        Test if the sample is an undetermined sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • isIndexedSample

        public boolean isIndexedSample​(int sampleId)
        Test if the sample is an indexed sample.
        Parameters:
        sampleId - the sample id
        Returns:
        sequence index related to the lane and sample name

      • getProjectSample

        public String getProjectSample​(int sampleId)
        Get the project related to a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the project related to the sample

      • getSampleDescription

        public String getSampleDescription​(int sampleId)
        Get the description of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the description of the sample

      • getSampleGenome

        public String getSampleGenome​(int sampleId)
        Gets the sample genome.
        Parameters:
        sampleId - the sample id
        Returns:
        the sample genome

      • getNormalizedSampleGenome

        public String getNormalizedSampleGenome​(int sampleId)
        Gets the normalized sample genome.
        Parameters:
        sampleId - the sample id
        Returns:
        the normalized sample genome

      • getSampleIndex

        public String getSampleIndex​(int sampleId)
        Get the index of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the index of the sample

      • getSampleIndex2

        public String getSampleIndex2​(int sampleId)
        Get the index of a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the index of the sample

      • isLaneIndexed

        public boolean isLaneIndexed​(int lane)
        Checks if is lane indexed.
        Parameters:
        lane - the lane
        Returns:
        true, if is lane indexed

      • isLaneControl

        public boolean isLaneControl​(int sampleId)
        Check if the lane related to the sample name is a control lane.
        Parameters:
        sampleId - the sample Id
        Returns:
        true if the lane is a control otherwise false

      • getSampleId

        public int getSampleId​(int lane,
                       String demuxName)
        Get the identifier of sample from its lane and demuxmultiplexing name.
        Parameters:
        lane - the lane
        demuxName - the demultiplexing name
        Returns:
        the id of the sample or -1 if not found

      • getPooledSampleCount

        public int getPooledSampleCount()
        Get the pooled sample count.
        Returns:
        the pooled sample count

      • getPooledSampleDemuxName

        public String getPooledSampleDemuxName​(int pooledSampleId)
        Get the demultiplexing name of a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        the demultiplexing name of a pooled sample

      • getPooledSampleProjectName

        public String getPooledSampleProjectName​(int pooledSampleId)
        Get the project name of a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        the project name of a pooled sample

      • getPooledSampleProject

        public int getPooledSampleProject​(int pooledSampleId)
        Get the project id of a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        the project id of a pooled sample

      • getPooledSampleIndex

        public String getPooledSampleIndex​(int pooledSampleId)
        Get the index of a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        the index of a pooled sample

      • getPooledSampleDescription

        public String getPooledSampleDescription​(int pooledSampleId)
        Get the description of a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        the description of a pooled sample

      • getSamplesInPooledSample

        public List<Integer> getSamplesInPooledSample​(int pooledSampleId)
        Get the list of sample identifiers in a pooled sample.
        Parameters:
        pooledSampleId - the id of the pooled sample
        Returns:
        a list of sample identifiers

      • getAllPooledSamples

        public List<Integer> getAllPooledSamples()
        Get all samples ids (with undetermined samples) of the run.
        Returns:
        all samples related to the lane

      • getPooledSamples

        public List<Integer> getPooledSamples()
        Get all samples ids (without undetermined samples) of the run.
        Returns:
        all samples related to the lane

      • isUndeterminedPooledSample

        public boolean isUndeterminedPooledSample​(int pooledSampleId)
        Test if the sample is an undetermined sample.
        Parameters:
        pooledSampleId - the pooled sample id
        Returns:
        sequence index related to the lane and sample name

      • getProjectCount

        public int getProjectCount()
        Get the project count.
        Returns:
        the project count

      • getProjects

        public List<Integer> getProjects()
        Get all project identifiers of the run.
        Returns:
        all project identifiers of the run

      • getProjectName

        public String getProjectName​(int projectId)
        Get the name of a project.
        Parameters:
        projectId - the id of the project
        Returns:
        the name of a project

      • getProjectId

        public int getProjectId​(String projectName)
        Get the id of a project from its name.
        Parameters:
        projectName - the name of the project
        Returns:
        the id of the projet or -1 if not found

      • getSamplesInProject

        public List<Integer> getSamplesInProject​(int projectId)
        Get the list of the samples of a project.
        Parameters:
        projectId - the project id
        Returns:
        a list with the sample identifiers of the project

      • getReadCount

        public int getReadCount()
        Get the read count in run.
        Returns:
        read count.

      • getIndexedReadCount

        public int getIndexedReadCount()
        Get the indexed read count in run.
        Returns:
        indexed read count.

      • getLaneCount

        public int getLaneCount()
        Get the lane count in run.
        Returns:
        lane count

      • isReadIndexed

        public boolean isReadIndexed​(int read)
        Check if the read is indexed.
        Parameters:
        read - the read number
        Returns:
        true if the read is indexed,otherwise false

      • getRunTilesPerLane

        public int getRunTilesPerLane()
        Gets the run tiles per lane.
        Returns:
        the run tiles per lane

      • getRunMode

        public String getRunMode()
        Get the run mode.
        Returns:
        run mode

      • getSequencerName

        public String getSequencerName()
        Gets the sequencer name.
        Returns:
        the sequencer name

      • getSequencerFamily

        public String getSequencerFamily()
        Gets the sequencer family.
        Returns:
        the sequencer name

      • getSequencerApplicationName

        public String getSequencerApplicationName()
        Gets the sequencer application name.
        Returns:
        the sequencer application name

      • getSequencerApplicationVersion

        public String getSequencerApplicationVersion()
        Gets the sequencer application version.
        Returns:
        the sequencer application version

      • getSequencerRTAVersion

        public String getSequencerRTAVersion()
        Gets the RTA version.
        Returns:
        the RTA version

      • getBcl2FastqVersion

        public String getBcl2FastqVersion()
        Gets the bcl2fastq version.
        Returns:
        the bcl2fastq version

      • getReadCyclesCount

        public int getReadCyclesCount​(int read)
        Get the cycles count in the read.
        Parameters:
        read - the read number
        Returns:
        cycles count in the read

      • getFlowcellId

        public String getFlowcellId()
        Gets the flowcell id.
        Returns:
        the flowcell id

      • getSampleRawClusterCount

        public int getSampleRawClusterCount​(int sampleId,
                                    int read)
        Get the raw cluster count for a sample.
        Parameters:
        sampleId - the sampleId
        read - the read
        Returns:
        the raw cluster count of the sample

      • getSamplePFClusterCount

        public int getSamplePFClusterCount​(int sampleId,
                                   int read)
        Get the passing filter cluster count for a sample.
        Parameters:
        sampleId - the sample id
        read - the read
        Returns:
        the passing filter cluster count of the sample

      • getTilesCount

        public int getTilesCount()
        Get the tiles count.
        Returns:
        tiles count

      • getReadPrcAlign

        public double getReadPrcAlign​(int lane,
                              int read)
        Get the percent align Phix related to the lane and the read.
        Parameters:
        lane - the lane number
        read - the read number
        Returns:
        percent align Phix related to the lane and the read

      • getReadRawClusterCount

        public long getReadRawClusterCount​(int lane,
                                   int read)
        Get the raw cluster count related to a lane and a read.
        Parameters:
        lane - the lane number
        read - the read number
        Returns:
        the raw cluster count related to a lane and a read

      • getReadPFClusterCount

        public long getReadPFClusterCount​(int lane,
                                  int read)
        Get the passing filter cluster count related to a lane and a read.
        Parameters:
        lane - the lane number
        read - the read number
        Returns:
        the passing filter cluster count related to a lane and a read

      • getSampleRawClusterRecoveryCount

        public int getSampleRawClusterRecoveryCount​(int sampleId)
        Get the raw cluster recovery count for a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the raw cluster recovery count of the sample

      • getSamplePFClusterRecoveryCount

        public int getSamplePFClusterRecoveryCount​(int sampleId)
        Get the passing filter cluster recovery count for a sample.
        Parameters:
        sampleId - the sample id
        Returns:
        the passing filter cluster recovery count of the sample

      • getLaneRawClusterRecoveryCount

        public int getLaneRawClusterRecoveryCount​(int lane)
        Get the raw cluster recovery count for a lane.
        Parameters:
        lane - the lane
        Returns:
        the raw cluster recovery count of the lane

      • getLanePFClusterRecoveryCount

        public int getLanePFClusterRecoveryCount​(int lane)
        Get the passing filter cluster recovery count for a lane.
        Parameters:
        lane - the lane
        Returns:
        the passing filter cluster recovery count of the lane

      • getPercentMappedReadOnContaminationSample

        public double getPercentMappedReadOnContaminationSample​(int sampleId,
                                                        int read)
        Get the percent mapped read on dataset contaminants.
        Parameters:
        sampleId - the sample Id
        read - the read number
        Returns:
        the percent mapped read on dataset contaminants.

      • get

        public String get​(String key)
        Get a key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • get

        public String get​(String key,
                  String defaultValue)
        Get a key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getBoolean

        public boolean getBoolean​(String key)
        Get a boolean key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • getBoolean

        public boolean getBoolean​(String key,
                          boolean defaultValue)
        Get a boolean key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getInt

        public int getInt​(String key)
        Get an integer key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • getInt

        public int getInt​(String key,
                  int defaultValue)
        Get an integer key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getLongArray

        public long[] getLongArray​(String key)
        Get an longTable key.
        Parameters:
        key - key name
        Returns:
        the table of values of the data for the key

      • getLongArray

        public long[] getLongArray​(String key,
                           long[] defaultValue)
        Get a long array key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getLong

        public long getLong​(String key)
        Get a long key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • getLong

        public long getLong​(String key,
                    long defaultValue)
        Get a long key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getFloat

        public float getFloat​(String key)
        Get a float key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • getFloat

        public float getFloat​(String key,
                      float defaultValue)
        Get a float key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • getDouble

        public double getDouble​(String key)
        Get a double key.
        Parameters:
        key - key name
        Returns:
        the value of the data for the key

      • getDouble

        public double getDouble​(String key,
                        double defaultValue)
        Get a double key.
        Parameters:
        key - key name
        defaultValue - value to use if the key does not exist
        Returns:
        the value of the data for the key

      • put

        public void put​(String key,
                String value)
        Set a key.
        Parameters:
        key - key to set
        value - value of the key

      • put

        public void put​(String key,
                boolean boolValue)
        Set a key with a boolean value.
        Parameters:
        key - key to set
        boolValue - value of the key

      • put

        public void put​(String key,
                int intValue)
        Set a key with an integer value.
        Parameters:
        key - key to set
        intValue - value of the key

      • put

        public void put​(String key,
                long longValue)
        Set a key with a long value.
        Parameters:
        key - key to set
        longValue - value of the key

      • put

        public void put​(String key,
                float floatValue)
        Set a key with a float value.
        Parameters:
        key - key to set
        floatValue - value of the key

      • put

        public void put​(String key,
                double doubleValue)
        Set a key with a double value.
        Parameters:
        key - key to set
        doubleValue - value of the key

      • put

        public void put​(String key,
                String... strings)
        Set a key with an array of strings as value.
        Parameters:
        key - key to set
        strings - list of the key

      • put

        public void put​(String key,
                long... longs)
        Set a key with an array of longs as value.
        Parameters:
        key - key to set
        longs - list of the key

      • put

        public void put​(String key,
                Collection<String> strings)
        Set a key with a collection of strings as value.
        Parameters:
        key - key to set
        strings - set of the key

      • put

        public void put​(RunData data)
        Set the key and values of a RunData object in the current RunData.
        Parameters:
        data - Data to add

      • contains

        public boolean contains​(String key)
        Test if the RunData contains a key.
        Parameters:
        key - key name
        Returns:
        true if the RunData object contains the key

      • remove

        public void remove​(String key)
        Remove a key from the Rundata.
        Parameters:
        key - key name

      • removeIfExists

        public void removeIfExists​(String key)
        Remove a key from the Rundata if the key exists.
        Parameters:
        key - key name

      • size

        public int size()
        Get the number of entries in RunData.
        Returns:
        the number of entries

      • createRunDataFile

        public void createRunDataFile​(String fileName)
                       throws IOException
        Create the data file.
        Parameters:
        fileName - path destination
        Throws:
        IOException - Signals that an I/O exception has occurred.

      • createRunDataFile

        public void createRunDataFile​(File fileName)
                       throws IOException
        Create the data file.
        Parameters:
        fileName - file destination
        Throws:
        IOException - Signals that an I/O exception has occurred.

      • addDataFileInRundata

        public void addDataFileInRundata​(String fileName)
                          throws IOException
        Add the data file in the rundata.
        Parameters:
        fileName - file source
        Throws:
        IOException - if an error occurs while reading the data file

      • addDataFileInRundata

        public void addDataFileInRundata​(File file)
                          throws IOException
        Add the data file in the rundata.
        Parameters:
        file - file source
        Throws:
        IOException - if an error occurs while reading the data file

      • print

        public void print()
        Print the content of the object on standard output.

      • getMap

        public Map<String,​String> getMap()
        Gets the map.
        Returns:
        the map